GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FHA - FHA domain
Pfam: PF00498 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0357
Length: 68
Sequences: 6556
Seq/Len: 96.41
HH_delta: -0.136 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
26_S36_E1.658282.620
27_F33_F1.656712.617
47_N63_D1.641572.593
32_Q58_P1.482572.342
24_R38_L1.46672.317
24_R36_E1.427232.255
37_D40_S1.362282.152
36_E56_P1.337742.113
35_I44_T1.25071.976
2_T9_C1.245371.967
23_A35_I1.243651.965
60_K63_D1.182821.869
9_C12_V1.10831.751
34_Y58_P1.09561.731
3_I23_A1.092021.725
26_S34_Y1.01241.599
28_D34_Y0.997941.577
40_S43_G0.971041.534
45_F50_R0.919851.453
8_D21_R0.912021.441
18_I67_F0.886121.400
2_T10_D0.86851.372
23_A67_F0.854271.350
19_S42_N0.839161.326
37_D43_G0.834561.318
37_D44_T0.795971.258
6_S20_R0.770571.217
35_I65_I0.763691.207
2_T21_R0.730751.154
45_F66_R0.716671.132
27_F30_D0.694041.096
5_R19_S0.687151.086
5_R20_R0.669011.057
26_S56_P0.660581.044
43_G50_R0.655241.035
9_C21_R0.643311.016
28_D32_Q0.642351.015
21_R38_L0.620290.980
2_T24_R0.58960.931
29_D32_Q0.55680.880
48_G66_R0.539440.852
19_S41_T0.520940.823
49_Q57_V0.516110.815
3_I25_I0.516010.815
46_V51_L0.500740.791
6_S12_V0.497850.787
20_R41_T0.493220.779
13_L18_I0.487760.771
36_E53_P0.482930.763
3_I11_I0.482720.763
34_Y56_P0.467830.739
19_S40_S0.446170.705
48_G64_I0.442660.699
6_S21_R0.441580.698
46_V65_I0.432070.683
46_V57_V0.429210.678
19_S22_H0.426350.674
6_S9_C0.424220.670
2_T38_L0.417530.660
5_R42_N0.416010.657
22_H43_G0.410470.648
27_F32_Q0.405730.641
51_L57_V0.402210.635
53_P57_V0.390720.617
18_I22_H0.386240.610
44_T51_L0.385740.609
23_A44_T0.380310.601
28_D56_P0.37340.590
47_N65_I0.365970.578
30_D58_P0.361460.571
7_P39_G0.359420.568
57_V63_D0.354730.560
19_S43_G0.350370.554
3_I67_F0.347650.549
22_H37_D0.3360.531
9_C13_L0.321680.508
16_P66_R0.318870.504
20_R42_N0.318320.503
34_Y53_P0.316980.501
17_S20_R0.315660.499
27_F34_Y0.314790.497
7_P11_I0.311890.493
22_H42_N0.302250.478
59_L63_D0.301860.477
12_V23_A0.300830.475
12_V16_P0.296550.469
46_V63_D0.294060.465
16_P20_R0.293220.463
58_P61_D0.285870.452
40_S44_T0.285570.451
13_L67_F0.282720.447
25_I35_I0.281510.445
35_I51_L0.281090.444
3_I13_L0.272470.430
25_I65_I0.270150.427
36_E52_G0.264270.418
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
4h87A199.5-0.136
2ff4A0.955999.5-0.094
3elvA199.5-0.094
2jpeA199.4-0.086
2cswA199.4-0.086
2pieA199.4-0.082
3elsA199.4-0.078
1qu5A0.985399.4-0.073
4jonA0.985399.4-0.07
1g3gA0.985399.4-0.069

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